Category Archives: Networks and Systems

Lack of replication no surprise when we’re studying really complex problems

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All opinions are my own and do not necessarily reflect those of Novo Nordisk

For another nice take on this topic see Paul Knoepfler’s blog post here.

One of the sacred (can I say sacred in reference to something scientific?) tenets of the scientific method is reproducibility.  If something is real and measurable, if it’s a fact of the material world, then the expectation is that the result should be reproducible by another experimenter using the same methods as described in the original report.  One of the most well known (among physicists anyway) examples of irreproducible data is the Valentine’s Day Magnetic Monopole detected by Blas Cabrera back in 1982.  Great experimental data.  Never repeated, and therefore viewed as insufficient proof for the existence of a magnetic monopole.

So it’s troubling that in the past few years there have been numerous stories about the lack of reproducibility for different scientific experiments.  In biomedical science the number of  reports on the difficulty of reproducing results has gotten so great that the NIH has begun thinking about how to confirm and require reproducibility of some kinds of experimental results.  Just a few days ago another field, that of psychological priming, saw the publication of an article that the effects of “high-performance priming,” could not be reproduced.  This is another field undergoing serious questioning about whether/why results don’t reproduce, with commentary from such luminaries as Daniel Kahneman. Continue reading →

What does the Hela genome agreement imply for consent and genome data usage?

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All opinions my own and do not necessarily reflect those of Novo Nordisk.

A fair amount of reporting (for example here, here and here) has gone into the recent news that the NIH and the descendants of Henrietta Lacks have reached an agreement about the conditions under which the genome sequence of the HeLa cell line will be shared.  The basic parameters are that researchers wanting access to the data will need to apply for permission, the application committee will include members of the Lacks family, any publications will acknowledge the contribution of the Henrietta Lacks, and future genome sequences will be submitted to dbGAP.

This is a generally welcome development, and in no small part due to the work of Rebecca Skloot.  Her book, The Immortal Life of Henrietta Lacks provided the impetus to the current developments by popularizing the story of Ms. Lacks and the cell line derived from her tissues.  However, this agreement also can be seen as a precedent of sorts, and the future implications for the ethics of consent, genetic information sharing and genomic research are unclear.

Whose genome is it, anyway?

In Pasco Phronesis, David Bruggeman penned a post on some of the possible implications.  He discusses one of the key elements of genetic consent that I generally haven’t seen elaborated on much in the current literature: familial consent and exposure.   To what extent do those who share part of a sequenced genome have a say in the granting and rescinding of consent for the usage of genetic information?   Continue reading →

Finding an Alka Seltzer for the oceans

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All opinions are my own and do not necessarily reflect those of Novo Nordisk
Some time ago I wrote an article for Real Change (reposted here) about research being done at the University of Washington to understand the effects of ocean acidification due to rising atmospheric carbon dioxide levels.  The rising pH of the oceans is another one in my list of things we don’t worry enough about with climate change but really should.  Like the bees.  It’s such a seemingly tiny, subtle thing.  The measured decrease in pH of maybe 0.1 units is due to ocean waters absorbing atmospheric CO2 and the resulting conversion of some of that to carbonic acid.  Seems small but it’s really a big deal.
Scientists have documented apparent effects of ocean acidity on coral reefs and oysters, among other organisms (abstracts from links; articles behind paywalls), and while oyster farmers can try to add antacids to their spawning beds, the oceans as a whole are a bit large for a local solution.  Which is why I was excited to see the Paul Allen Family Foundation post the current submissions to their Ocean Challenge (HT @deirdrelockwood).
Let me provide a disclaimer that I have not read most of these proposals in depth.  However, scanning through the titles and sampling a few in greater detail, it’s clear that the Ocean Challenge has prompted a number of groups to come up with ideas about how to try and monitor, test, and mitigate the effects of ocean acidification, at least at the local level and in some cases on a grander scale.  The proposals are available online for public comment, and finalists selected in September.
There are a couple of things to really like about this.   All the proposal summaries are devoid of names and affiliations, which may lead to more unbiased evaluations by public commentators.  This is something that’s been debated for years with respect to other granting agencies like the NIH.  Another great thing is that this is open–anyone can apply and everyone’s ideas are out there for others to learn from, debate, and expand upon.  I’m a fan of open source science, and transparency, and this feels like it’s in that vein.  And last, this is really a big problem.  Not to say government agencies aren’t funding and studying this, but as we’ve seen with other private non-profit foundations like the Gates Foundation, there is a third way beyond government and private industry to try and effect policy and make changes.  I hope for success from this effort.  Because I would really miss oysters.

Why everyone should worry (more) about the bees

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All opinions are my own and do not necessarily reflect those of Novo Nordisk.

Among my personal top list of things people really should be more worried about with respect to how we’re changing the environment, the decline of bees is close to number one.  On some days, like when I’m biting into a delicious Rainier cherry or a luscious peach, the decline of bees is number one.    And I’m not saying this topic hasn’t gotten any press or concern.  On the contrary, there’s been plenty.  I just also think it should have more.

So imagine the jolt to my already heightened sense of worry when I saw the following two studies.  This one, in Nature (abstract only, article behind a paywall), puts forth a theoretical model of what happens when a species goes “functionally extinct.”  By this, the authors mean the point at which the number of members of a given species in an ecosystem declines to the point that other species are affected and may themselves go fully extinct.  It turns out that in interconnected food webs, as a given species declines in numbers, it affects other species’ overall survival as well, and that most often the species going really and truly extinct is not the one initially declining.

I think of this situation as being kind of like playing in a massively multiplayer online role-playing game like Star Wars: The Old Republic, and you’re in a team with several others, each of whom has his or her role.  Often the healer of the party gets damaged quickly in a fight, but they’re not the first one to go down.  Instead, it’s the damage-dealing specialists who find themselves getting beat up and dying when the healing falters.  The team, the network, relies on every member functioning fully to succeed, and reducing performance by one part of the team can have unintended consequences.

Well, that was a tortured analogy.

But the point with respect to bees is how just the decline of bee populations alone may be having cascading effects on the ecosystems in which they operate.

Another take on the importance of different species and diversity in networks comes from this study in the Proceeding of the National Academy of Sciences (USA) (abstract only, article behind a paywall).  In this situation, the researchers tested the idea that plant community and insect networks are robust enough to survive the loss of individual species.  They located subalpine meadow plots and carefully removed all members of a single pollinator species and asked what would happen.  Network robustness theory would suggest other pollinators would take the place of the removed species, which previously served a specific niche.  And this happened.  However, the overall health of the plant community nevertheless appeared potentially threatened since this meant pollinators carried more types of pollen, leading to less efficiency in pollinating any given plant species.

These studies are just two of many that describe the unexpected and unintended consequences of changes in ecosystem communities.  All kinds of changes.  Like the decline of frogs and other amphibians, which I also worry about.  My personal bias towards worrying about bees probably stems from my perception of the crucial role they play in so many functions, both for humankind in specific and ecosystems in general.  The Nature paper also suggests the scary thought that we might be missing the forest for the bees, and the real impact of bee declines has already happened in the extinction of other, interconnected species which we may never know about, because they might already be gone.

When a grand old scientist talks, you listen: Maynard Olson and Genomic Medicine

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All opinions are my own and do not necessarily reflect those of Novo Nordisk.

Last night I had the great opportunity to hear Maynard Olson give a public lecture on Genomic Medicine.  As one of the founders of the Human Genome Project, he’s been around in a pivotal role for much of the revolution in our understanding of the genome.  A revolution, as he himself points out, that we are still just beginning.

He gave his speech as part of the UW Genome Sciences Department’s summer lecture series, and spoke to a packed auditorium about how the information we are learning about the genome has implications for diagnostics, therapeutics, and public policy.  I’ve heard Maynard speak before, and he’s always refreshingly down-to-earth, candid and measured in his descriptions and comments.  Not for him are flights of speculation or hyperbole, and he actually ended his talk with a call to stop the hype.  As he said, “The product is solid.  It doesn’t need hype.”  Maynard, who is slim, with a fringe of red hair that’s silvering at the sides (kind of like Reed Richards), does not look at all near his age of about seventy years. Continue reading →